生物技术通报 ›› 2023, Vol. 39 ›› Issue (4): 157-165.doi: 10.13560/j.cnki.biotech.bull.1985.2022-0832
薛皦(), 朱庆锋, 冯彦钊, 陈沛, 刘文华, 张爱霞, 刘勤坚, 张琪, 于洋()
收稿日期:
2022-07-05
出版日期:
2023-04-26
发布日期:
2023-05-16
通讯作者:
于洋,男,博士,副研究员,研究方向:作物遗传资源发掘与创新利用;E-mail: yuyang@gdaas.cn作者简介:
薛皦,女,博士,助理研究员,研究方向:植物抗病分子生物学;E-mail: xuejiao@gdaas.cn
基金资助:
XUE Jiao ZHU Qing-feng FENG Yan-zhao CHEN Pei LIU Wen-hua ZHANG Ai-xia LIU Qin-jian ZHANG Qi YU Yang()
Received:
2022-07-05
Published:
2023-04-26
Online:
2023-05-16
摘要:
上游开放阅读框(upstream open reading frame, uORF)是一类能够精确控制蛋白质翻译的mRNA元件,位于mRNA的5'端前导区,主要通过抑制翻译起始来调节下游主体开放阅读框(main open reading frame, mORF)的翻译。目前对植物uORF的预测和鉴定主要集中于生物信息学和翻译组学鉴定技术。植物uORF广泛参与调节生长发育、营养代谢、抗病免疫等多个生命活动过程。本文对植物uORF的分类、功能机制、预测和鉴定方法、植物规避uORF的方式以及植物uORF的工程应用等进行综述归纳,旨在更系统和深入地理解植物uORF的功能与机制,并为uORF应用于作物分子育种工作提供参考。
薛皦, 朱庆锋, 冯彦钊, 陈沛, 刘文华, 张爱霞, 刘勤坚, 张琪, 于洋. 植物基因上游开放阅读框的研究进展[J]. 生物技术通报, 2023, 39(4): 157-165.
XUE Jiao ZHU Qing-feng FENG Yan-zhao CHEN Pei LIU Wen-hua ZHANG Ai-xia LIU Qin-jian ZHANG Qi YU Yang. Advances in Upstream Open Reading Frame in Plant Genes[J]. Biotechnology Bulletin, 2023, 39(4): 157-165.
图1 植物uORF分类 A:uORF独立于mORF; B:uORF终止于mORF读码框内; C:uORF和mORF终止位置相同; D:混合型uORF
Fig. 1 Upstream open reading frame(uORF)classifica-tions in plant A: The location of the stop codon of the uORF is independent of the mORF. B: The stop codon of the uORF overlaps with the mORF. C: The stop codon of the uORF is the same as that of the stop codon of the mORF. D: Multiple uORFs
图2 植物uORF对mORF的调控方式 A:核糖体渗漏扫描; B:核糖体在mORF处重起始翻译; C:核糖体解离; D:NMD
Fig. 2 Regulatory mechanisms of uORF to mORF A: Leaky scanning by 40S ribosome subnit. B: Translational reinitiation at mORF. C: Ribosome dissociates from the mRNA; D: Trigger nonsense-mediated mRNA decay(NMD)
方法比较 Comparison of methods | 多聚核糖体分析技术 Polysome profiling | 核糖体-新生肽链复合物测序 RNC-Seq | 核糖体图谱分析技术 Ribo-seq | 核糖体亲和纯化技术 RAP |
---|---|---|---|---|
分离原理 | 蔗糖密度梯度离心 | 单一浓度蔗糖溶液离心 | RNA酶降解未被核糖体覆盖的mRNA后经蔗糖梯度离心 | 亲和标签免疫沉淀 |
分离对象 | 多聚核糖体复合物 | 核糖体-新生肽链复合物 | 被核糖体覆盖保护的RNA小片段 | 核糖体大亚基及其结合的mRNA |
优点 | 可对核糖体数分组进行收集分析 | RNA回收容易,得率高 | 准确度高,通量大 | 可组织特异性检测 |
检测方法 | 高通量测序或芯片技术 | 高通量测序或芯片技术 | 高通量测序 | 高通量测序或芯片技术 |
检测的mRNA长度 | 全长 | 全长 | 被核糖体覆盖的约30 nt | 全长 |
缺点 | 仪器贵重、操作繁琐、RNA回收难度大、纯度低 | 仪器贵重、无法分析结合不同数量核糖体的 mRNA | 操作复杂、酶切条件难控制 | 需构建转基因植株 |
表1 预测uORF的实验方法比较
Table 1 Comparison of the methods for predicting uORFs
方法比较 Comparison of methods | 多聚核糖体分析技术 Polysome profiling | 核糖体-新生肽链复合物测序 RNC-Seq | 核糖体图谱分析技术 Ribo-seq | 核糖体亲和纯化技术 RAP |
---|---|---|---|---|
分离原理 | 蔗糖密度梯度离心 | 单一浓度蔗糖溶液离心 | RNA酶降解未被核糖体覆盖的mRNA后经蔗糖梯度离心 | 亲和标签免疫沉淀 |
分离对象 | 多聚核糖体复合物 | 核糖体-新生肽链复合物 | 被核糖体覆盖保护的RNA小片段 | 核糖体大亚基及其结合的mRNA |
优点 | 可对核糖体数分组进行收集分析 | RNA回收容易,得率高 | 准确度高,通量大 | 可组织特异性检测 |
检测方法 | 高通量测序或芯片技术 | 高通量测序或芯片技术 | 高通量测序 | 高通量测序或芯片技术 |
检测的mRNA长度 | 全长 | 全长 | 被核糖体覆盖的约30 nt | 全长 |
缺点 | 仪器贵重、操作繁琐、RNA回收难度大、纯度低 | 仪器贵重、无法分析结合不同数量核糖体的 mRNA | 操作复杂、酶切条件难控制 | 需构建转基因植株 |
图3 植物规避uORF调节的方式 A:选择可变转录起始位点; B:可变剪切排除或修剪uORF; C:不依赖于5'帽子结构的翻译起始
Fig. 3 Mechanisms for evading uORF-mediated regulation A: Alternative transcription start site(TSS)selection. B: Processing uORF by alternative splicing. C: Cap-independent translational initiation
图4 应用uORF操控基因翻译 A:删除uORF上游及翻译起始序列; B:编辑突变uORF的翻译起始位点; C:基因工程手段利用uORF序列
Fig. 4 Manipulation of gene translation by editing uORFs A: Involved the deletion of uORF upstream sequence and initiation codon. B: Involved the mutation of uORF initiation codon. C: Utilized uORF sequence by genetic engineering
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